Hello; Some assumptions have been made. Possibly correct but not known for sure. One such, mine, is that the medications added to the tank are what killed off the BB. If correct such means the BB colonies will need to be reestablished essentially from scratch. Depending on your actions this can take several weeks. I go back to you somehow getting a starter culture of BB from somewhere. That being getting some colonies of bb from an established aquarium. Maybe snails if you like snails as i suspect the BB could be on the shells. I am not so confident that plants hold BB colonies. Any solid object from an old tank ought the have the BB. The BB are sessile which I understand means they form sticky colonies on surfaces. My take is they are not in the water to any great degree, so old tank water is not likely to be useful. Getting a starter culture can speed things up.
Another assumption, not mine, is by throwing out the detritus loaded filter floss that too much of the BB are removed. The notion being you are getting an ammonia spike because a significant portion of the BB are suddenly removed. If this is the case there will be plenty of BB on other surfaces of the tank to both rebuilt the numbers and continuee to eat up the ammonia & nitrite.
(Note- you can get ammonia spikes other ways. A common way is to add a lot of new small fish or a few big fish. New fish = more ammonia. A thing to keep in mind is the BB will come into balance with the amount of ammonia present. Kepp a steady amount (biomass) of fish and the BB population will match that. Over feed and the decay process will add some ammonia. Add or remove fish and the BB population adjusts. An ongoing process.)
I do not think you have an ammonia spike at this point.
Regardless I think you need to keep up an accelerated WC schedule or be willing to sacrifice the current fish in order to enhance the "fish-in" cycle method. Sadly, the affected fish are damaged to a degree already.
Around ten years ago a 55 gallon tank kept having outbreaks of what I think was a cyanobacteria algae. Formed sheets of algae which would cover everything. I finally broke the tank down. Took all the fish out into buckets. Put the gravel and all other equipment in buckets and soaked in a Clorox solution. Put the plants in a bucket with an antibiotic solution. Filled the tank and put Clorox in the water.
Put it all back together after doing lots and lots and lots of rinsing of gravel and all. Added plants and some doses of PRIME. Threw in some snails from a clean tank for the first few days. When temps and such were normal added fish a few at a time while also throwing in a sponge filter from a clean tank. I hope you do not face that much work. I still wonder about long term residuals from the medication or some other factor not yet discovered.